Merge pull request #45 from hobrien/master

Unphased SNPs triggering 'unable to parse genotype' warning
bmvdgeijn · May 31, 2016 · c2509a4 · c2509a4
2 parents 467651c + 7b30418
commit c2509a4
Showing 1 changed file with 7 additions and 5 deletions.
diff --git a/snp2h5/vcf.c b/snp2h5/vcf.c
@@ -172,11 +172,13 @@ void vcf_parse_haplotypes(VCFInfo *vcf_info, char *haplotypes,
  /* try with '/' separator instead */
  n = sscanf(inner_tok, "%d/%d", &hap1, &hap2);
 
- if(n == 2 && warn_phase) {
- my_warn("%s:%d: some genotypes are unphased (delimited "
- "with '/' instead of '|')\n", __FILE__, __LINE__,
- inner_tok);
- warn_phase = FALSE;
+ if(n == 2) {
+ if(warn_phase) {
+ my_warn("%s:%d: some genotypes are unphased (delimited "
+ "with '/' instead of '|')\n", __FILE__, __LINE__,
+ inner_tok);
+ warn_phase = FALSE;
+ }
  } else {
  my_warn("%s:%d: could not parse genotype string '%s'\n",
  __FILE__, __LINE__, inner_tok);